[English] 日本語
Yorodumi
- PDB-3su0: Crystal structure of NS3/4A protease variant R155K in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3su0
TitleCrystal structure of NS3/4A protease variant R155K in complex with danoprevir
ComponentsGenome polyprotein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / NS3 / drug resistance / drug design / Protease inhibitors / HCV / serine protease / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / ribonucleoprotein complex / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily ...Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Trypsin-like serine proteases / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Thrombin, subunit H / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-TSV / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus subtype 1a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.159 Å
AuthorsSchiffer, C.A. / Romano, K.P.
CitationJournal: Plos Pathog. / Year: 2012
Title: The Molecular Basis of Drug Resistance against Hepatitis C Virus NS3/4A Protease Inhibitors.
Authors: Romano, K.P. / Ali, A. / Aydin, C. / Soumana, D. / Ozen, A. / Deveau, L.M. / Silver, C. / Cao, H. / Newton, A. / Petropoulos, C.J. / Huang, W. / Schiffer, C.A.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8844
Polymers20,9931
Non-polymers8913
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.279, 58.537, 60.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Genome polyprotein


Mass: 20992.844 Da / Num. of mol.: 1 / Mutation: L1039E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus subtype 1a / Strain: BID-V318 / Gene: NS3-NS4A / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8DG50
#2: Chemical ChemComp-TSV / (2R,6S,12Z,13aS,14aR,16aS)-6-[(tert-butoxycarbonyl)amino]-14a-[(cyclopropylsulfonyl)carbamoyl]-5,16-dioxo-1,2,3,5,6,7,8 ,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-2-yl 4-fluoro-2H-isoindole-2-carboxylate / ITMN-191 / danoprevir


Mass: 729.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H44FN5O9S / Comment: inhibitor*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE COFACTOR 4A RESIDUES 990-1000 (GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY ...THE COFACTOR 4A RESIDUES 990-1000 (GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY CORRESPOND TO RESIDUES NUMBERING 1678-1688 OF DATABASE SEQUENCE REFERENCE (UNP A8DG50). THIS PEPTIDE IS COVALENTLY LINKED TO THE N-TERMINUS OF NS3. C1679S MUTATION WAS ENGINEERED TO PREVENT DISULFIDE FORMATION. THE V1686I AND I1687N WERE ENGINEERED TO OPTIMIZE THE LINKER BETWEEN THE COFACTOR 4A AND NS3.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 295 K / Method: hanging drop, vapor diffusion / pH: 6.2
Details: 20-25% PEG 3350, 0.1M MES (pH 6.5), 4% ammonium sulfate, hanging drop, vapor diffusion, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.159→50 Å / Num. obs: 67429 / % possible obs: 97.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.055 / Χ2: 1.018 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.159-1.24.70.47161500.995190.4
1.2-1.255.80.40765881.007197.6
1.25-1.315.90.31366851.029198
1.31-1.3860.22967221.029198.4
1.38-1.4660.16567631.012198.6
1.46-1.576.10.11267571.002199.2
1.57-1.736.10.08168351.019199.4
1.73-1.9860.0768781.023199.8
1.98-2.560.05869701.0291100
2.5-505.80.03370811.025197.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M5M CHAIN B

3m5m


Resolution: 1.159→40.84 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1821 / WRfactor Rwork: 0.1624 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9084 / SU B: 0.96 / SU ML: 0.02 / SU R Cruickshank DPI: 0.0342 / SU Rfree: 0.0335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1718 3391 5 %RANDOM
Rwork0.1527 ---
obs0.1537 67223 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 51.75 Å2 / Biso mean: 12.6627 Å2 / Biso min: 4.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.71 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.159→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 57 192 1667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221559
X-RAY DIFFRACTIONr_bond_other_d0.0010.021034
X-RAY DIFFRACTIONr_angle_refined_deg1.3232.0082145
X-RAY DIFFRACTIONr_angle_other_deg1.08332537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05622.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59215235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2091512
X-RAY DIFFRACTIONr_chiral_restr0.0770.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211759
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02308
X-RAY DIFFRACTIONr_mcbond_it1.1181.51002
X-RAY DIFFRACTIONr_mcbond_other0.3721.5415
X-RAY DIFFRACTIONr_mcangle_it1.80621617
X-RAY DIFFRACTIONr_scbond_it2.5153557
X-RAY DIFFRACTIONr_scangle_it3.634.5514
X-RAY DIFFRACTIONr_rigid_bond_restr0.94132593
LS refinement shellResolution: 1.159→1.189 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 244 -
Rwork0.223 4115 -
all-4359 -
obs--86.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6806-3.12262.007210.33097.372810.5360.2294-0.20090.1653-0.77490.0058-0.4727-0.6166-0.3139-0.23520.1478-0.02050.11930.0063-0.00330.00778.1606-20.602-1.9348
20.5121-0.3568-0.49721.97261.15642.11160.0078-0.02690.02310.02230.0343-0.0761-0.04640.0464-0.04220.01640.00040.00430.01320.00360.00773.3238-1.74620.3724
31.3731-0.5072-1.44571.41190.14222.47470.028-0.09330.0126-0.0571-0.0018-0.061-0.04940.093-0.02630.0257-0.0060.00810.01050.0010.00973.86485.351819.6832
42.0225-2.66570.39615.56022.50567.7540.0117-0.0906-0.0315-0.4860.1358-0.7137-0.42120.4442-0.14760.0479-0.01510.1170.00860.01890.137312.7706-5.729711.8583
515.76641.966-2.0612.20260.02754.97990.1016-0.36090.11310.1216-0.069-0.0737-0.09780.229-0.03270.0243-0.0137-0.00960.0091-0.0010.01266.0095-1.821326.6117
61.34370.96610.83981.62181.6875.73690.02320.11050.0494-0.08960.0376-0.04020.0089-0.0286-0.06080.03060.00980.00650.03060.01010.0124-0.0586-5.336813.0482
71.3049-0.64310.67340.5253-1.05713.48680.00110.00470.02330.00640.002-0.00590.0512-0.0199-0.00320.0259-0.001800.01220.00370.0132-1.6212-7.734823.0324
80.0313-0.106-0.15090.13620.20260.2416-0.01220.0094-0.02360.0172-0.01070.00080.0255-0.00840.02290.030.00520.00360.0211-0.00010.0275-2.6988-14.134519.0085
92.62151.57661.27371.83510.81161.62970.0345-0.0373-0.0681-0.0043-0.0313-0.14830.03740.057-0.00320.01010.00810.01440.02280.0030.034110.956-12.945816.2503
100.99650.35310.13840.27230.19830.468-0.0107-0.0108-0.01630.0296-0.0135-0.01090.02370.01040.02410.02370.00530.0030.01260.00230.0217-0.4288-17.89421.5853
118.9961.4526-6.82391.0531-0.6655.1594-0.0986-0.2784-0.13980.014-0.0219-0.05230.03730.18730.12050.02050.0125-0.01430.0469-0.00140.0074-0.9035-8.244434.5206
121.88851.308-2.22020.79-1.70584.6090.0041-0.03240.1817-0.01290.00980.10330.01580.0393-0.0140.01640.00780.01180.0073-0.00040.0513-11.22020.113226.8616
132.2060.8115-1.00270.3787-0.18060.84420.0895-0.00050.17650.0440.01650.04570.0314-0.085-0.10590.0141-0.00710.01550.03930.00370.032-18.302-4.142229.8656
140.5733-0.5002-0.20861.1685-0.44551.33720.03630.0045-0.032-0.03260.06020.1474-0.0372-0.1583-0.09660.01740.01250.01210.03650.02660.0377-21.6307-2.332225.0416
151.351-0.77782.46024.1295-1.00880.75240.0058-0.0683-0.00430.13490.0994-0.09620.0159-0.062-0.10520.01250.0190.00780.05150.03820.0204-15.47131.623515.5025
160.12790.0323-0.7837-0.0914-0.09883.73260.0228-0.01330.1048-0.01570.02250.055-0.0290.0892-0.04520.0218-0.00070.01590.0352-0.00920.0891-8.5626-4.537930.1663
171.7699-0.75471.49830.8965-0.63952.98970.0274-0.01110.0344-0.015-0.0654-0.02010.0698-0.04890.03790.0197-0.00390.00470.03310.00040.01-12.5428-9.124521.211
180.7911-0.0847-0.48883.3187-4.19796.5586-0.10460.1607-0.058500.25160.23980.0791-0.367-0.1470.0149-0.01930.00540.07110.02090.0338-22.575-3.351117.0994
193.8205-2.10822.25411.9167-2.26693.9744-0.0067-0.0304-0.04680.01120.07980.05740.0893-0.084-0.07310.0264-0.00120.00840.01470.00240.0091-12.455-13.139128.3253
2016.1308-0.758-5.60091.2569-1.0930.415-0.4827-0.4678-0.43960.0271-0.02090.03380.02280.07750.50360.0650.03690.01770.0020.04750.1307-5.2878-19.218430.5966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A983 - 988
2X-RAY DIFFRACTION2A989 - 1003
3X-RAY DIFFRACTION3A1004 - 1012
4X-RAY DIFFRACTION4A1013 - 1027
5X-RAY DIFFRACTION5A1028 - 1033
6X-RAY DIFFRACTION6A1034 - 1041
7X-RAY DIFFRACTION7A1042 - 1049
8X-RAY DIFFRACTION8A1050 - 1061
9X-RAY DIFFRACTION9A1062 - 1070
10X-RAY DIFFRACTION10A1071 - 1088
11X-RAY DIFFRACTION11A1089 - 1100
12X-RAY DIFFRACTION12A1101 - 1111
13X-RAY DIFFRACTION13A1112 - 1122
14X-RAY DIFFRACTION14A1123 - 1129
15X-RAY DIFFRACTION15A1130 - 1136
16X-RAY DIFFRACTION16A1137 - 1152
17X-RAY DIFFRACTION17A1153 - 1157
18X-RAY DIFFRACTION18A1158 - 1167
19X-RAY DIFFRACTION19A1168 - 1173
20X-RAY DIFFRACTION20A1174 - 1179

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more